Sodium in PDB 5v1g: Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus

All present enzymatic activity of Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus:
2.7.7.7;

The structure of Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus, PDB code: 5v1g was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.88 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.380, 79.240, 54.880, 90.00, 105.49, 90.00
R / Rfree (%)	18.7 / 22.7

The binding sites of Sodium atom in the Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus (pdb code 5v1g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus, PDB code: 5v1g:

Sodium binding site 1 out of 1 in the Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta Binary Complex with 8-Oxog at the Primer Terminus within 5.0Å range: probe atom residue distance (Å) B Occ D:Na101 b:46.0 occ:1.00 O D:HOH215 2.2 24.9 1.0 O A:HOH558 2.3 31.4 1.0 O D:HOH225 2.3 31.6 1.0 OP2 D:DT2 2.7 12.2 1.0 O A:HOH666 2.9 39.6 1.0 O5' D:DT2 3.6 14.7 1.0 P D:DT2 3.7 16.1 1.0 N A:THR67 4.0 17.5 1.0 C6 D:DT2 4.3 12.9 1.0 C7 D:DT2 4.3 14.1 1.0 C2' D:DG1 4.3 13.7 1.0 O D:HOH220 4.4 20.7 1.0 CB A:THR67 4.5 27.6 1.0 C2' D:DT2 4.5 19.5 1.0 CA A:GLY66 4.6 14.0 1.0 CG A:LYS68 4.6 19.4 1.0 N A:LYS68 4.6 13.5 1.0 O A:HOH706 4.7 40.9 1.0 C5 D:DT2 4.7 12.5 1.0 C A:GLY66 4.8 16.1 1.0 OP1 D:DT2 4.8 13.4 1.0 CA A:THR67 4.8 16.4 1.0 O3' D:DG1 4.8 14.0 1.0 O D:HOH216 4.9 25.3 1.0 C3' D:DT2 4.9 14.2 1.0 C3' D:DG1 4.9 14.3 1.0 C5' D:DT2 4.9 11.6 1.0 OG1 A:THR67 5.0 27.6 1.0

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293